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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MITOCHONDRIAL DNA PACKAGING PROTEIN ABF2P IN COMPLEX WITH DNA AT 2.6 ANGSTROM RESOLUTION
 
Authors :  A. Chakraborty, S. Lyonnais, M. Sola
Date :  20 Apr 16  (Deposition) - 08 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  Dna Binding Protein Dna Packaging, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chakraborty, S. Lyonnais, F. Battistini, A. Hospital, G. Medici, R. Prohens, M. Orozco, J. Vilardell, M. Sola
Dna Structure Directs Positioning Of The Mitochondrial Genome Packaging Protein Abf2P.
Nucleic Acids Res. V. 45 951 2017
PubMed-ID: 27899643  |  Reference-DOI: 10.1093/NAR/GKW1147

(-) Compounds

Molecule 1 - ARS-BINDING FACTOR 2, MITOCHONDRIAL
    Chains: A, D, G, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCRI7A (PET-28A DERIVATIVE)
    Expression System Taxid: 469008
    Expression System Variant: PLYS
    Expression System Vector Type: PLASMID
    Gene: ABF2, HIM1, YMR072W, YM9916.11
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
 
Molecule 2 - DNA (5'- D(*TP*TP*TP*AP*TP*TP*AP*TP*TP*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*A)- 3')
    Chains: B, E, H, K
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: OLIGOS PURCHASED FROM BIOMERS
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*AP*AP*AP*TP*AP*AP*TP*AP*AP*A)- 3')
    Chains: C, F, I, L
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: OLIGOS PURCHASED FROM BIOMERS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO G:119 , GLY G:121 , TYR G:169 , DT H:6binding site for residue ACT G 201
2AC2SOFTWAREPRO G:66binding site for residue ACT G 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JGH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JGH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JGH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JGH)

(-) Exons   (0, 0)

(no "Exon" information available for 5JGH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jgh A  27 KASKRTQLRNELIKQGPKRPTSAYFLYLQDHRSQFVKENPTLRPAEISKIAGEKWQNLEADIKEKYISERKKLYSEYQKAKKEFDEKLPPKKPAGPFIKYANEVRSQVFAQHPDKSQLDLMKIIGDKWQSLDQSIKDKYIQEYKKAIQEYNARYPL 182
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      


Chain B from PDB  Type:DNA  Length:22
                                                      
                 5jgh B   1 TTTATTATTTTATATTATATAA  22
                                    10        20  


Chain C from PDB  Type:DNA  Length:22
                                                      
                 5jgh C   1 TTATATAATATAAAATAATAAA  22
                                    10        20  


Chain D from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jgh D  27 KASKRTQLRNELIKQGPKRPTSAYFLYLQDHRSQFVKENPTLRPAEISKIAGEKWQNLEADIKEKYISERKKLYSEYQKAKKEFDEKLPPKKPAGPFIKYANEVRSQVFAQHPDKSQLDLMKIIGDKWQSLDQSIKDKYIQEYKKAIQEYNARYP 181
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     


Chain E from PDB  Type:DNA  Length:22
                                                      
                 5jgh E   1 TTTATTATTTTATATTATATAA  22
                                    10        20  


Chain F from PDB  Type:DNA  Length:22
                                                      
                 5jgh F   1 TTATATAATATAAAATAATAAA  22
                                    10        20  


Chain G from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jgh G  27 KASKRTQLRNELIKQGPKRPTSAYFLYLQDHRSQFVKENPTLRPAEISKIAGEKWQNLEADIKEKYISERKKLYSEYQKAKKEFDEKLPPKKPAGPFIKYANEVRSQVFAQHPDKSQLDLMKIIGDKWQSLDQSIKDKYIQEYKKAIQEYNARYPL 182
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      


Chain H from PDB  Type:DNA  Length:22
                                                      
                 5jgh H   1 TTTATTATTTTATATTATATAA  22
                                    10        20  


Chain I from PDB  Type:DNA  Length:22
                                                      
                 5jgh I   1 TTATATAATATAAAATAATAAA  22
                                    10        20  


Chain J from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jgh J  31 RTQLRNELIKQGPKRPTSAYFLYLQDHRSQFVKENPTLRPAEISKIAGEKWQNLEADIKEKYISERKKLYSEYQKAKKEFDEKLPPKKPAGPFIKYANEVRSQVFAQHPDKSQLDLMKIIGDKWQSLDQSIKDKYIQEYKKAIQEYNARYP 181
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain K from PDB  Type:DNA  Length:22
                                                      
                 5jgh K   1 TTTATTATTTTATATTATATAA  22
                                    10        20  


Chain L from PDB  Type:DNA  Length:22
                                                      
                 5jgh L   1 TTATATAATATAAAATAATAAA  22
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JGH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JGH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JGH)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  5jgh
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  ABF2_YEAST | Q02486
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        ABF2_YEAST | Q02486: 5jh0

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